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- PDB-1b45: ALPHA-CNIA CONOTOXIN FROM CONUS CONSORS, NMR, 43 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1b45
TitleALPHA-CNIA CONOTOXIN FROM CONUS CONSORS, NMR, 43 STRUCTURES
ComponentsALPHA-CNIA
KeywordsTOXIN / ALPHA-CONOTOXIN / CONUS CONSORS / NICOTINIC ACETYLCHOLINE RECEPTOR
Function / homology
Function and homology information


host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Conotoxin, alpha-type / Alpha conotoxin precursor / Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature.
Similarity search - Domain/homology
Alpha-conotoxin CnIA
Similarity search - Component
Biological speciesConus consors (invertebrata)
MethodSOLUTION NMR / HIGH TEMPERATURE SIMULATED ANNEALING
AuthorsFavreau, P. / Krimm, I. / Le Gall, F. / Bobenrieth, M.J. / Lamthanh, H. / Bouet, F. / Servent, D. / Molgo, J. / Menez, A. / Letourneux, Y. / Lancelin, J.M.
CitationJournal: Biochemistry / Year: 1999
Title: Biochemical characterization and nuclear magnetic resonance structure of novel alpha-conotoxins isolated from the venom of Conus consors.
Authors: Favreau, P. / Krimm, I. / Le Gall, F. / Bobenrieth, M.J. / Lamthanh, H. / Bouet, F. / Servent, D. / Molgo, J. / Menez, A. / Letourneux, Y. / Lancelin, J.M.
History
DepositionJan 5, 1999Processing site: BNL
Revision 1.0Jul 9, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-CNIA


Theoretical massNumber of molelcules
Total (without water)1,5491
Polymers1,5491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)43 / 80POTENTIAL ENERGIES
Representative

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Components

#1: Protein/peptide ALPHA-CNIA


Mass: 1548.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus consors (invertebrata) / References: UniProt: P56973
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121TOCSY
131NOESY

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Sample preparation

DetailsContents: 90%WATER/ 10%D2O
Sample conditionspH: 4.1 / Pressure: 1 atm / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AVANCE DRX500 / Manufacturer: Bruker / Model: AVANCE DRX500 / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: HIGH TEMPERATURE SIMULATED ANNEALING / Software ordinal: 1
Details: A TOTAL OF 80 STRUCTURES WERE GENERATED STARTING FROM RANDOM COORDINATES BY A HIGH TEMPERATURE SIMULATED ANNEALING PROTOCOL AT 1000K (NILGES ET AL., 1988), USING THE PARALLHDG.PRO FORCE ...Details: A TOTAL OF 80 STRUCTURES WERE GENERATED STARTING FROM RANDOM COORDINATES BY A HIGH TEMPERATURE SIMULATED ANNEALING PROTOCOL AT 1000K (NILGES ET AL., 1988), USING THE PARALLHDG.PRO FORCE FIELD OF X-PLOR THAT DO NO TAKE INTO ACCOUNT THE ATTRACTIVE TERM OF THE VAN DER WALLS' INTERACTIONS NOR THE ELECTROSTATIC INTERACTIONS. THE STRUCTURES THAT AGREED WITH THE FORCE FIELD AND EXPERIMENTAL RESTRAINTS (NO NOE VIOLATION GRATER THAN 0.2 A) WERE FURTHER REFINED, USING THE FULL CHARMM22 FORCE FIELD OF X-PLOR. AN APPROXIMATE SOLVENT ELECTROSTATIC SCREENING EFFECT WAS INTRODUCED BY USING A DISTANCE-DEPENDENT DIELECTRIC CONSTANT AND BY REDUCING THE ELECTRIC CHARGES OF THE FORMALLY CHARGED AMINO ACID SIDE CHAINS (ARG, LYS AND HIS) AND THE N-TERMINUS TO 20% OF THEIR NOMINAL CHARGES DEFINED IN THE CHARMM22 FORCE FIELD. AFTER 1500 STEPS OF CONJUGATE GRADIENT ENERGY MINIMIZATION, THE DYNAMIC WAS INITIATED AT 750 K, EQUILIBRATED FOR 0.5 PS WITH 1 FS INTEGRATION STEPS, THEN COUPLED TO A HEAT BATH AT 750 K AND THE MOLECULE WAS ALLOWED TO EVOLVE FOR 10 PS BEFORE BEING COOLED SLOWLY TO 300 K ON A PERIOD OF 5.4 PS AND ALLOWED TO EVOLVE AGAIN AT THIS TEMPERATURE FOR 15 PS. AT THE END, STRUCTURES WERE ENERGY MINIMIZED BY 1500 STEPS OF THE CONJUGATE GRADIENT ALGORITHM. THE FORCE CONSTANT USED FOR THE NOE POTENTIAL IN BOTH STEPS WAS 50 KCAL MOL-1 A-2.
NMR ensembleConformer selection criteria: POTENTIAL ENERGIES / Conformers calculated total number: 80 / Conformers submitted total number: 43

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